LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.1472000 3.1472000 3.1472000 Created orthogonal box = (0.0000000 -50.747075 0.0000000) to (25.373537 50.747075 3.1472000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.5132590 3.5132590 3.1472000 Created 260 atoms using lattice units in orthogonal box = (0.0000000 -50.747075 0.0000000) to (25.373537 50.747075 3.1472000) create_atoms CPU = 0.002 seconds 260 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.5132590 3.5132590 3.1472000 Created 261 atoms using lattice units in orthogonal box = (0.0000000 -50.747075 0.0000000) to (25.373537 50.747075 3.1472000) create_atoms CPU = 0.001 seconds 261 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 9 33 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 521 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_424746498193_002#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 9 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.465 | 4.465 | 4.465 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3376.0644 0 -3376.0644 100421.71 55 0 -3538.5656 0 -3538.5656 8611.7925 Loop time of 0.60127 on 1 procs for 55 steps with 521 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3376.06435984079 -3538.56236599272 -3538.56563846861 Force two-norm initial, final = 231.24298 0.29679745 Force max component initial, final = 58.919668 0.10611306 Final line search alpha, max atom move = 1.0000000 0.10611306 Iterations, force evaluations = 55 102 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.5835 | 0.5835 | 0.5835 | 0.0 | 97.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0094184 | 0.0094184 | 0.0094184 | 0.0 | 1.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008352 | | | 1.39 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3834.00 ave 3834 max 3834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 30478.0 ave 30478 max 30478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30478 Ave neighs/atom = 58.499040 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 9 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.462 | 4.462 | 4.462 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -3538.5656 0 -3538.5656 8611.7925 8104.8758 61 0 -3538.8269 0 -3538.8269 -20.319626 8127.9921 Loop time of 0.0613149 on 1 procs for 6 steps with 521 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3538.56563846861 -3538.82681054265 -3538.82690947641 Force two-norm initial, final = 112.09150 0.67511538 Force max component initial, final = 111.24413 0.18845273 Final line search alpha, max atom move = 0.00048795427 9.1956317e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.056992 | 0.056992 | 0.056992 | 0.0 | 92.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00094666 | 0.00094666 | 0.00094666 | 0.0 | 1.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003376 | | | 5.51 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3422.00 ave 3422 max 3422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 30452.0 ave 30452 max 30452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30452 Ave neighs/atom = 58.449136 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 9 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.601 | 4.601 | 4.601 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3538.8269 0 -3538.8269 -20.319626 Loop time of 7.106e-06 on 1 procs for 0 steps with 521 atoms 225.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 7.106e-06 | | |100.00 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3479.00 ave 3479 max 3479 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 30398.0 ave 30398 max 30398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30398 Ave neighs/atom = 58.345489 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 9 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.601 | 4.601 | 4.601 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -3538.8269 -3538.8269 25.345502 102.00436 3.1438633 -20.319626 -20.319626 -37.10645 -22.20441 -1.6480166 2.5762737 262.76796 Loop time of 7.106e-06 on 1 procs for 0 steps with 521 atoms 323.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 7.106e-06 | | |100.00 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3479.00 ave 3479 max 3479 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15199.0 ave 15199 max 15199 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 30398.0 ave 30398 max 30398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30398 Ave neighs/atom = 58.345489 Neighbor list builds = 0 Dangerous builds = 0 521 -3538.82690947641 eV 2.57627368839579 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00 Potential info: Mo potential Atomic number: 42 Potential info: Mo potential Atomic number: 42